Louisa's "unmanageable thoughts" seem to emerge when she looks into the fire, which she does at various points in the novel, which appears to allow Louisa to think about various topics that are troubling her. In the quote you cite, for example, Louisa says to Tom that looking into the fire helps her to "wonder" about the future that she and Tom will face when they are "grown up." Of course, when her mother hears about the determination of Louisa's "unmanageable thoughts" that "will wonder," we can understand more of why she has them:
"Then I beg of you, Louisa... to do nothing of that description, for goodness' sake you inconsiderate girl, or I shall never hear the last of it from your father."
Wondering is not allowed in the facts-dominated world in which their father is raising them, and so Louisa's wonderings are repressed and have become these "unmanageable thoughts" precisely because they do not fit into the facts-based world which she knows. Having had no experience of dealing with emotions and fancy, she has no idea what to do with the natural instinct within her to wonder.